LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 1
  using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units        electron
dimension    3
boundary     p p p
atom_style   atomic
atom_modify  map yes
pair_style   none

# Time step (in femtoseconds)
timestep     0.5

# Temperature (in Kelvin)
variable     Temp equal 17.4

# Force constant (in Hartree energies per Bohr radius squared)
variable     k equal 1.2154614120000001e-08

# Number of beads
variable     Nbeads equal 4
variable     ibead uloop ${Nbeads} pad
variable     ibead uloop 4 pad
variable     seed equal 18889

# Create box and atoms. All distances are in Bohr
region       box block -1500 1500 -1500 1500 -1500 1500
create_box   1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  1 by 1 by 1 MPI processor grid
variable     a loop 3
label        loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop

# Electron mass (in amu)
mass         1 0.00054858

# Initialize velocities
velocity     all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 188892 mom yes rot yes dist gaussian

# Add harmonic external force
fix          harm all spring/self ${k}
fix          harm all spring/self 1.215461412e-08

# Add harmonic potential energy to total energy and potential energy
fix_modify   harm energy yes

# PIMD command
fix          pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix          pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no

# Outputs
variable prim_kinetic  equal f_pimdb[5]
variable virial        equal f_pimdb[6]

thermo_style custom step pe v_virial v_prim_kinetic
thermo          1

run             100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
   Step         PotEng        v_virial    v_prim_kinetic
         0   0              1.3661449e-08  0.0009918329 
         1   7.3810761e-10  1.8742641e-09  0.00099182267
         2   3.0654593e-09  7.1801177e-09  0.00099180053
         3   6.4534507e-09  1.4372388e-08  0.00099176038
         4   1.1681892e-08  3.1274072e-08  0.00099170266
         5   1.8404818e-08  5.2470231e-08  0.00099162511
         6   2.6171374e-08  7.2301291e-08  0.00099153   
         7   3.5990441e-08  9.5440683e-08  0.00099141194
         8   4.9770229e-08  1.1669162e-07  0.00099127168
         9   6.6159035e-08  1.3551097e-07  0.00099109846
        10   8.7281867e-08  1.6050328e-07  0.00099089759
        11   1.1505206e-07  1.8645705e-07  0.0009906735 
        12   1.4564491e-07  2.1181418e-07  0.00099042271
        13   1.8674942e-07  2.4218941e-07  0.00099012073
        14   2.3275077e-07  2.7507982e-07  0.00098977876
        15   2.833552e-07   3.1771012e-07  0.00098940169
        16   3.3078875e-07  3.6075963e-07  0.00098900826
        17   3.7783787e-07  4.0059005e-07  0.00098859985
        18   4.3007763e-07  4.3883585e-07  0.00098817535
        19   4.8592613e-07  4.8036287e-07  0.00098770764
        20   5.4429898e-07  5.2362451e-07  0.00098721266
        21   6.0140068e-07  5.7705077e-07  0.00098670407
        22   6.6036274e-07  6.3271105e-07  0.00098617081
        23   7.3748601e-07  6.9382916e-07  0.00098557406
        24   8.1086859e-07  7.5979853e-07  0.0009849612 
        25   8.8638234e-07  8.232213e-07   0.00098434971
        26   9.8252709e-07  8.9901705e-07  0.0009836645 
        27   1.0768657e-06  9.7033126e-07  0.0009830068 
        28   1.1810654e-06  1.0444697e-06  0.00098229311
        29   1.2964318e-06  1.1208219e-06  0.00098150213
        30   1.4097624e-06  1.1899315e-06  0.00098077686
        31   1.5368367e-06  1.2560026e-06  0.00098003518
        32   1.6777082e-06  1.3287355e-06  0.00097921099
        33   1.8186759e-06  1.399856e-06   0.0009784037 
        34   1.9730383e-06  1.4769272e-06  0.00097754491
        35   2.1285065e-06  1.5642459e-06  0.00097667479
        36   2.2809575e-06  1.6571388e-06  0.00097572641
        37   2.4393024e-06  1.7603492e-06  0.00097475881
        38   2.6212592e-06  1.8666516e-06  0.00097373763
        39   2.8115312e-06  1.9696572e-06  0.0009727081 
        40   3.0115212e-06  2.0910539e-06  0.00097155807
        41   3.2325069e-06  2.2198868e-06  0.00097030871
        42   3.4582526e-06  2.3576614e-06  0.00096896762
        43   3.6838101e-06  2.496284e-06   0.00096760456
        44   3.9267475e-06  2.637657e-06   0.00096619083
        45   4.1942569e-06  2.795845e-06   0.00096470693
        46   4.4694976e-06  2.9727162e-06  0.00096303835
        47   4.7570486e-06  3.1451673e-06  0.00096140406
        48   5.0917213e-06  3.3241907e-06  0.00095971129
        49   5.4581889e-06  3.5094834e-06  0.00095790964
        50   5.8607381e-06  3.7049195e-06  0.00095603039
        51   6.2673583e-06  3.9139587e-06  0.0009540918 
        52   6.6764632e-06  4.1289537e-06  0.0009520767 
        53   7.0828028e-06  4.3481079e-06  0.00095003676
        54   7.4858144e-06  4.5702968e-06  0.00094802906
        55   7.8711706e-06  4.7928135e-06  0.00094600351
        56   8.2756726e-06  5.0253448e-06  0.0009438419 
        57   8.6667628e-06  5.2569331e-06  0.00094169256
        58   9.0585083e-06  5.4997767e-06  0.00093948055
        59   9.4634766e-06  5.7547729e-06  0.00093714003
        60   9.8696653e-06  6.0074589e-06  0.00093480857
        61   1.0308345e-05  6.2647899e-06  0.00093244785
        62   1.0757919e-05  6.5384938e-06  0.00092998209
        63   1.1183568e-05  6.8124372e-06  0.00092751453
        64   1.1585073e-05  7.0913777e-06  0.00092505171
        65   1.1993605e-05  7.3773956e-06  0.00092256944
        66   1.2382612e-05  7.6811232e-06  0.00091984092
        67   1.2768116e-05  7.9951107e-06  0.0009170037 
        68   1.3181941e-05  8.3096758e-06  0.00091414977
        69   1.3605472e-05  8.6232285e-06  0.00091137219
        70   1.4027012e-05  8.9388929e-06  0.00090857909
        71   1.4471706e-05  9.2524846e-06  0.00090583473
        72   1.4896833e-05  9.5688611e-06  0.00090308342
        73   1.5345003e-05  9.8873586e-06  0.00090026584
        74   1.5779905e-05  1.0203245e-05  0.00089755256
        75   1.6189898e-05  1.0523755e-05  0.00089485804
        76   1.6654778e-05  1.0848398e-05  0.00089217189
        77   1.7131363e-05  1.1164286e-05  0.00088956967
        78   1.7572176e-05  1.1466652e-05  0.00088700311
        79   1.8000817e-05  1.177381e-05   0.00088439373
        80   1.838117e-05   1.2059606e-05  0.00088199635
        81   1.8762432e-05  1.233837e-05   0.0008797438 
        82   1.9099052e-05  1.261531e-05   0.00087745162
        83   1.9507863e-05  1.2899972e-05  0.00087506863
        84   1.9885648e-05  1.3160246e-05  0.00087288444
        85   2.0266439e-05  1.3438712e-05  0.00087052617
        86   2.0612316e-05  1.372546e-05   0.00086818634
        87   2.0959061e-05  1.4017631e-05  0.00086572407
        88   2.13065e-05    1.4328439e-05  0.000862992  
        89   2.1634898e-05  1.4640964e-05  0.00086017364
        90   2.2023174e-05  1.4978644e-05  0.0008570595 
        91   2.2431573e-05  1.5307214e-05  0.00085411601
        92   2.2872283e-05  1.5649328e-05  0.00085112325
        93   2.338476e-05   1.6015833e-05  0.0008479391 
        94   2.3912199e-05  1.6393131e-05  0.00084474237
        95   2.437725e-05   1.674573e-05   0.00084165639
        96   2.4828999e-05  1.7094435e-05  0.00083858996
        97   2.5286762e-05  1.7451741e-05  0.00083536142
        98   2.5769956e-05  1.780703e-05   0.00083221292
        99   2.624134e-05   1.8141862e-05  0.00082913227
       100   2.6731735e-05  1.8457846e-05  0.00082619877
Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms

Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
88.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 1.773e-06  | 1.773e-06  | 1.773e-06  |   0.0 |  0.15
Comm    | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 |   0.0 |  1.27
Output  | 0.00021888 | 0.00021888 | 0.00021888 |   0.0 | 18.58
Modify  | 0.00086503 | 0.00086503 | 0.00086503 |   0.0 | 73.42
Other   |            | 7.754e-05  |            |       |  6.58

Nlocal:              3 ave           3 max           3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:00
